Analysis of whole genomes using mapping by admixture linkage disequilibrium (MALD), and of candidate genes requires an appropriate set of markers and the ability to accurately genotype hundreds to thousands of patients with hundreds to thousands of markers. Utilizing the laboratory we have developed at the Laboratory of Genomic Diversity (LGD) has allowed determination and publication of a MALD map for disease gene discovery in African Americans. Our collaborators have now used that map and method for gene localization in prostate cancer and multiple sclerosis. Ongoing efforts in the laboratory are applying the MALD technology to HIV/AIDS, Hepatitis C virus (HCV), focal segmental glomerulosclerosis, and end-stage renal disease.The laboratory has also undertaken candidate gene analysis. One success from this year was the publication of a incidence density sampling approach to HIV-1 infection. In this study we examined genes in the CCR5 viral entry pathway. An invited commentary was glowing in pointing to the approach as the way genetic epidemiological studies regarding viral infection should be designed and performed.